import nglview as nv

import Bio
from Bio import PDB, SeqIO, SeqUtils, Align
parser = PDB.PDBParser()

import warnings
from Bio import BiopythonWarning
warnings.simplefilter('ignore', BiopythonWarning)

prot = nv.show_file('data/3hpb.pdb')
prot

prot = nv.show_pdbid('3hpb')
prot

structure = parser.get_structure('7aiz', 'data/7aiz.pdb')
prot_struct = nv.show_biopython(structure)
prot_struct

from rdkit import Chem
from rdkit.Chem import AllChem

mol = Chem.MolFromSmiles('O[C@H]1[C@H](O)[C@@H](COP(O)(O)=O)OC(O)[C@@H]1O')
mol = Chem.AddHs(mol) # add H's
AllChem.EmbedMolecule(mol) # generate 3D structure

G6P = nv.show_rdkit(mol)
G6P

prot_3hpb = nv.show_file('data/3hpb.pdb')
prot_3hpb.clear_representations()
prot_3hpb.add_representation('ball+stick', selection='protein')
prot_3hpb

prot_3hpb = nv.show_file('data/3hpb.pdb')
prot_3hpb.clear_representations()
prot_3hpb.add_representation('licorice', selection='protein')
prot_3hpb

prot_1rpy = nv.show_file('data/3hpb.pdb')
prot_1rpy.add_representation('licorice', selection='sidechains')
prot_1rpy

prot_1rpy = nv.show_file('data/3hpb.pdb')
prot_1rpy.clear_representations()
prot_1rpy.add_representation('cartoon', color='hydrophobicity')
prot_1rpy

prot_1rpy = nv.show_file('data/3hpb.pdb')
prot_1rpy.add_representation('licorice', color='hydrophobicity')
prot_1rpy

prot_1rpy = nv.show_file('data/3hpb.pdb')
prot_1rpy.clear_representations()
prot_1rpy.add_representation('cartoon', color='sstruc')
prot_1rpy

prot_1rpy = nv.show_file('data/3hpb.pdb')
prot_1rpy.add_representation('licorice', color='resname')
prot_1rpy

full_surface = nv.show_biopython(structure)
full_surface.add_surface(opacity=0.3)
full_surface

acidic = nv.show_file('data/8pfy.cif')
acidic.clear_representations()
acidic.add_representation('licorice')
acidic.add_surface(selection='acidic',
                   opacity=0.4, 
                   color='pink')
acidic

acidbase = nv.show_biopython(structure)
acidbase.clear_representations()
acidbase.add_representation('licorice')
acidbase.add_surface(selection=':B and backbone and (basic or acidic)',
                   opacity=0.3, 
                   color='lightblue')
acidbase